Bug 755098 – [science overlay] sci-biology/khmer-1.0.1 : lib/read_parsers.cc: error: operand type bool* is incompatible with argument 1 of _sync_and_and_fetch

• Status: RESOLVED FIXED
• Product: Gentoo Linux

[Description Toralf Förster 2020-11-17 18:06:42 UTC]

x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -fno-diagnostics-color -fPIC -DVERSION=1.0.1 -DNDEBUG=1 -UNO_UNIQUE_RC -Ilib -Ilib/zlib -Ilib/bzip2 -I/usr/include/python2.7 -c lib/read_parsers.cc -o /var/tmp/portage/sci-biology/khmer-1.0.1/work/khmer-1.0.1-python2_7/temp.linux-x86_64-2.7/lib/read_parsers.o
lib/read_parsers.cc: In member function ‘const bool khmer::read_parsers::IStreamReader::is_at_EOS_ATOMIC()’:
lib/read_parsers.cc:221:46: error: operand type ‘bool*’ is incompatible with argument 1 of ‘__sync_and_and_fetch’
  221 |     return __sync_and_and_fetch( &_at_eos, 1 );
      |                                              ^
error: command 'x86_64-pc-linux-gnu-g++' failed with exit status 1

  -------------------------------------------------------------------

  This is an unstable amd64 chroot image at a tinderbox (==build bot)
  name: 17.1_no-multilib-libressl_science-20201116-220441

  -------------------------------------------------------------------

gcc-config -l:
 [1] x86_64-pc-linux-gnu-10.2.0 *
/usr/lib/llvm/11
11.0.0
Available Python interpreters, in order of preference:
  [1]   python3.7
  [2]   python3.9 (fallback)
  [3]   python3.8 (fallback)
  [4]   python2.7 (fallback)

  timestamp(s) of HEAD at this tinderbox image:
/var/db/repos/gentoo	Tue Nov 17 03:35:37 PM UTC 2020
/var/db/repos/libressl	Sat Nov  7 03:06:11 PM UTC 2020

emerge -qpvO sci-biology/khmer
[ebuild  N    ] sci-biology/khmer-1.0.1  PYTHON_TARGETS="python2_7"

[Comment 1 Toralf Förster 2020-11-17 18:06:43 UTC]

Created attachment 671965 [details]
emerge-info.txt

[Comment 2 Toralf Förster 2020-11-17 18:06:44 UTC]

Created attachment 671968 [details]
emerge-history.txt

[Comment 3 Toralf Förster 2020-11-17 18:06:46 UTC]

Created attachment 671971 [details]
environment

[Comment 4 Toralf Förster 2020-11-17 18:06:47 UTC]

Created attachment 671974 [details]
etc.portage.tbz2

[Comment 5 Toralf Förster 2020-11-17 18:06:49 UTC]

Created attachment 671977 [details]
sci-biology:khmer-1.0.1:20201117-161400.log

[Comment 6 Toralf Förster 2020-11-17 18:06:51 UTC]

Created attachment 671980 [details]
temp.tbz2

[Comment 7 Lucas Mitrak 2021-06-08 16:51:29 UTC]

Created attachment 714699 [details]
emerge.log

[Comment 8 Lucas Mitrak 2021-06-08 16:51:43 UTC]

Created attachment 714702 [details]
emerge-history.txt

[Comment 9 Lucas Mitrak 2021-06-08 16:51:58 UTC]

Created attachment 714705 [details]
emerge --info

[Comment 10 Lucas Mitrak 2021-06-08 16:52:17 UTC]

Created attachment 714708 [details]
etc/portage

[Comment 11 Lucas Mitrak 2021-06-08 16:52:41 UTC]

Created attachment 714711 [details]
ebuildtester emerge log

[Comment 12 Lucas Mitrak 2021-06-08 16:55:46 UTC]

This bug report was filed for version 1.0.1 which no longer exists. The current version is 2.1.1 and compiles correctly on a clean and current gentoo stage3 image created using ebuildtester. Therefore this bug was fixed in commit https://github.com/gentoo/sci/commit/d7637214cd6c37456262bc62ff07eab1b1dae6b3#diff-ce7e173aba459faecf30173821dda5962a379554b808d36d5448581ae2f0eafb.